MOIL
MOIL [1] supports the usual set of tools for molecular modelling by classical mechanics, including energy calculations, energy minimization, molecular dynamics, and more. Code is available to simulate curve crossing within the Landau Zener model. Moil allows for reasonably straightforward conversion of PDB files to computable datasets (coordinate and energy templates).
MOIL includes Locally Enhanced Sampling Approach and reaction path and long time dynamics algorithms that are based on action optimization. Also included the recently developed milestoning approach for the calculation of kinetics and thermodynamics along a reaction coordinate. The integration of a coarse-grained model into moil is also a feature.